Hi, The sequences all have to be aligned in the same sequence window (see example in image below) - there is only one alignment ID. In other words, you have to actually create a sequence alignment before you can calculate % sequence identity. There are lots of ways you can get sequence alignments (download from databases, use other programs or web servers) but if you want a way to do it in ChimeraX, see the "sequence align" command. For example seq align #1/A,B #2/A ... to create a sequence alignment of model 1 chains A and B and model 2 chain A. Then you can calculate identity, for example seq identity 1 denominator nongap Please see the "sequence" command help for the options on these commands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#identity> I hope this helps, Elaine
On Jul 17, 2024, at 9:37 AM, NUR AIDA SAKINAH via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, If I want to use the sequence identity command for two or more different sequences, should the command look like this "sequence identity 1/A 1/B 2/B denominator nongap" ?
On Wed, 17 Jul 2024 at 06:49, NUR AIDA SAKINAH <nuraida14599@gmail.com> wrote: Oh, that’s how it works. Thank you so much Elaine!
On Wed, 17 Jul 2024 at 03:26, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi, If the sequence window title bar says "[ID: 1]" that means the alignment ID is just "1", not "alignment-1"
However, I don't understand what you are trying to calculate.
If you show only a single sequence as the alignment there is nothing to calculate the % identity with. You would need the alignment to contain two or more different sequences.
I hope this makes sense. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2024, at 2:49 AM, NUR AIDA SAKINAH via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hai, I want to use the sequence identity command in ChimeraX but in the log said "Missing or invalid "src1" argument: Expected alignment-id or [alignment-id]:sequence-name-or-number". The input I gave is "sequence identity alignment-1" after open the tools>sequence>show sequence viewer and then select model e.g. #1/a and it show the ID as [ID: 1] but i got error. How to solve this problem?
Hope ChimeraX teams can help. Thank you!
